Increased inputs of nutrients and acid anions to oligotrophic mountain lakes are contributing to ANC depression, elevated nitrate concentrations, shifts in nutrient limitation, and changes in the productivity and structure of aquatic communities. A need for stricter standards based on measurable ecological effects has been identified as an important step toward the long-term protection of mountain lakes. The objectives of this research were to link atmospheric deposition with acidification and eutrophication effects, develop critical loads and nutrient criteria, and assess status and trends of Sierra Nevada lakes. Investigation of multiple proxies of deposition, climate, acidification, and eutrophication indicated that early 20th century ANC decline in a Sierra Nevada lake is attributed to atmospheric deposition and the subsequent recovery in the late 20th century is attributed to the success of the Clean Air Act. Correlation analysis indicated ANC was correlated with atmospheric deposition indicators, but was not correlated with climate measures or productivity proxies. However, analyses looking more broadly across the landscape found a correlation with present day indicators of atmospheric deposition (SCPs) and ANC. These results indicate that not all lakes have fully recovered from acid deposition and stricter regulatory standards are needed. I aimed to link atmospheric deposition indicators with effects of eutrophication and acidification at a landscape scale and found that atmospheric deposition indicators were correlated with acidification, but not with eutrophication. Quantifying the relationship between nitrogen deposition and eutrophication across complex mountain landscapes is presently challenging, leading to the conclusion that critical loads based on acidification are a more robust approach. An acidification critical load was calculated based on 20th century ANC and acid deposition patterns and is 73.9 eq ha^-1 yr^-1 for acid anions, which translates to 0.68 kg-N ha^-1 yr^-1 and 1.2 kg-SO4 ha^-1 yr-1. Nitrogen criteria were calculated and ranged from were 0.33 - 0.89 µM (10% ED), 1.0 - 4.0 µM (50% ED), and 3.1 - 18 µM (90% ED). Application of criteria to Sierra Nevada lakes indicated the 10% effective dose was exceeded by 28-37 %, the 50% effective dose was exceeded by 18-29%, and the 90% effective dose was exceeded by 0.0-21%.